Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,312,410 T→C 29.5% R285R (CGT→CGC)  menA → 1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,312,4100TC29.5% 111.0 / 54.1 115R285R (CGT→CGC) menA1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
Reads supporting (aligned to +/- strand):  ref base T (42/39);  new base C (5/29);  total (47/68)
Fisher's exact test for biased strand distribution p-value = 1.77e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01

Only 100 of 125 total aligned reads displayed.

TGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAG  >  minE/2312343‑2312470
                                                                   |                                                            
tGGTGAAGCAAGCCCGTTATGTGATGCTGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:280314/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:2446551/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:2615744/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:2652246/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:775703/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:1273600/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:1604530/68‑1 (MQ=255)
tGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:505082/68‑1 (MQ=255)
 ggTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGt                                                              <  1:2839444/67‑1 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:1065705/1‑67 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:2058687/1‑67 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:3381423/1‑67 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:894753/1‑67 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:794946/1‑67 (MQ=255)
     aagcaagcCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTg                                                          >  1:1197333/1‑67 (MQ=255)
        caagcTCGTTATGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      >  1:307012/1‑68 (MQ=255)
        caagcTCGTTATGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      >  1:1900838/1‑68 (MQ=255)
        caagcTCGTTATGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      >  1:1897667/1‑68 (MQ=255)
        caagcTCGTTATGTGATGCGCGAAATGGACCAGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      >  1:2217961/1‑68 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:2322101/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:416609/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:3418069/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:2303027/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:3218482/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:1231152/69‑1 (MQ=255)
               gTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:120923/69‑1 (MQ=255)
                  aTGTGATGCTGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTa                                            >  1:182938/1‑68 (MQ=255)
                  aTGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTa                                            >  1:1847635/1‑68 (MQ=255)
                  aTGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTa                                            >  1:2942294/1‑68 (MQ=255)
                  aTGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTa                                            >  1:2522115/1‑68 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:464496/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:2712316/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:3002096/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:2637201/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:262153/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:569646/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:3254787/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:512902/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1116615/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:3401484/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:45277/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1957763/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1778580/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1456430/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1712837/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1289528/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1618322/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:2029107/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:1501989/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:225037/58‑1 (MQ=255)
                  aTGTGATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:2381579/58‑1 (MQ=255)
                      gATGCGCGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGCACTGTCaa                                                      <  1:654931/54‑1 (MQ=255)
                            ggAAATGGACCCGGTGGCTATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACct                                 >  1:904673/1‑69 (MQ=255)
                                        ggTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGtttt                     <  1:1144352/69‑1 (MQ=255)
                                        ggTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGtttt                     <  1:1498223/69‑1 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTa                                     >  1:952735/1‑52 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:3134377/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:3132410/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:2866577/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:1393316/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:2669139/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTa                    >  1:2516925/1‑69 (MQ=255)
                                         gTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGGTTTa                    >  1:1397259/1‑69 (MQ=255)
                                            gCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGt                                              <  1:3114575/40‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:1406837/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:371164/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:3404889/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:1304046/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:3338028/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:1198633/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:2387356/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:1724233/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:2910204/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:2037797/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:2810322/68‑1 (MQ=255)
                                              gATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:2528978/68‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:3188163/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:514373/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:1133171/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:1920587/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:1493382/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGata              <  1:2922717/69‑1 (MQ=255)
                                               aTGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:893534/67‑1 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:686352/1‑39 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:3083413/1‑39 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:3248845/1‑39 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:1286054/1‑39 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:634830/1‑39 (MQ=255)
                                                 gCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACt                                          >  1:1925026/1‑39 (MQ=255)
                                                    aCCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGTCTAACCTGCTGTTTGTTTTAGGGATATTc           >  1:979725/1‑67 (MQ=255)
                                                    aCCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAAcc                                  >  1:2206476/1‑44 (MQ=255)
                                                    aCCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTc           >  1:2750798/1‑67 (MQ=255)
                                                    aCCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTc           >  1:2457143/1‑67 (MQ=255)
                                                      cAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGa                <  1:1821535/60‑1 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:739977/1‑69 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:2758739/1‑69 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:2903696/1‑69 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:3111706/1‑69 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:957895/1‑69 (MQ=255)
                                                           cTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAg  >  1:1539255/1‑69 (MQ=255)
                                                                   |                                                            
TGGTGAAGCAAGCCCGTTATGTGATGCGGGAAATGGACCCGGTGGCGATGCGACCAATGCTGGAACGTACTGTCAAGGGAGCGTTACTGACTAACCTGCTGTTTGTTTTAGGGATATTCCTAAGCCAG  >  minE/2312343‑2312470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A